The basic principle is the same whether you play SH3 or SH4. The only real difference is the TDC's. That was the biggest thing I had trouble getting my head around when I first started playing SH4 after SH3. After much practice, the little light bulb has come on and I enjoy SH4 quite a bit.
I have noticed ships changing speeds but not near as often as you have said. It is frustrating but I've never read a book about the US boats in the Pacific(or any other submarines in any other theater) that there wasn't any frustration on the skipper's/kaluen's part.
I would suggest using the mission editor to set up some target practice. Set up one or two ships in the middle of nowhere, prewar so they don't panic when they see you, at a set speed. Put yourself ahead of and perpindicular to their track and practice, practice, practice.
Now you don't have to worry about speed changes, the target taking evasive manuevers, being attacked, etc.
You can change variables such as speed, range, and AOB as you wish as you gain experience.
Good luck and don't give up yet.